Development of sequence-based markers for seed protein content in pigeonpea

Obala, J and Saxena, R K and Singh, V K and Sameer Kumar, C V and Saxena, K B and Tongoona, P and Sibiya, J and Varshney, R K (2019) Development of sequence-based markers for seed protein content in pigeonpea. Molecular Genetics and Genomics (TSI), 294 (1). pp. 57-68. ISSN 1617-4615

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Abstract

Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P < 0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords: Seed protein content, Cajanus cajan, Whole-genome resequencing, Next generation sequencing, Sequence variants, Common variant analysis, Pigeonpea, Crop improvement, phenotyping
Subjects: Others > Crop Improvement
Mandate crops > Pigeonpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 12 Mar 2019 08:58
Last Modified: 12 Mar 2019 08:58
URI: http://oar.icrisat.org/id/eprint/11085
Official URL: http://dx.doi.org/10.1007/s00438-018-1484-8
Projects: UNSPECIFIED
Funders: UNSPECIFIED
Acknowledgement: Authors are thankful to the United States Agency for International Development (USAID) and ICRISAT for funding various projects related to pigeonpea genomics at ICRISAT. We also thank Mr. Aamir Khan (ICRISAT) for his help in processing the WGRS data and Ms. Anu Chitikineni (ICRISAT) for coordinating Sanger sequencing and primer ordering. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals. ICRISAT is a member of CGIAR Consortium.
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